Riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow

Alexander L. Cope; Felicity Anderson; John Favate; Michael Jackson; Amanda Mok; Anna Kurowska; Junchen Liu; Emma Mackenzie; Vikram Shivakumar; Peter Tilton; Sophie M. Winterbourne; Siyin Xue; Kostas Kavoussanakis; Liana F. Lareau; Premal Shah; Edward W.J. Wallace

doi:10.1093/bioinformatics/btac093

Riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow

Alexander L. Cope, Felicity Anderson, John Favate, Michael Jackson, Amanda Mok, Anna Kurowska, Junchen Liu, Emma Mackenzie, Vikram Shivakumar, Peter Tilton, Sophie M. Winterbourne, Siyin Xue, Kostas Kavoussanakis, Liana F. Lareau, Premal Shah, Edward W.J. Wallace

School of Arts and Sciences, Genetics

Research output: Contribution to journal › Article › peer-review

Abstract

Motivation: Ribosome profiling, or Ribo-seq, is the state-of-the-art method for quantifying protein synthesis in living cells. Computational analysis of Ribo-seq data remains challenging due to the complexity of the procedure, as well as variations introduced for specific organisms or specialized analyses. Results: We present riboviz 2, an updated riboviz package, for the comprehensive transcript-centric analysis and visualization of Ribo-seq data. riboviz 2 includes an analysis workflow built on the Nextflow workflow management system for end-to-end processing of Ribo-seq data. riboviz 2 has been extensively tested on diverse species and library preparation strategies, including multiplexed samples. riboviz 2 is flexible and uses open, documented file formats, allowing users to integrate new analyses with the pipeline.

Original language	English (US)
Pages (from-to)	2358-2360
Number of pages	3
Journal	Bioinformatics
Volume	38
Issue number	8
DOIs	https://doi.org/10.1093/bioinformatics/btac093
State	Published - Apr 15 2022

All Science Journal Classification (ASJC) codes

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btac093

Cite this

Cope, A. L., Anderson, F., Favate, J., Jackson, M., Mok, A., Kurowska, A., Liu, J., Mackenzie, E., Shivakumar, V., Tilton, P., Winterbourne, S. M., Xue, S., Kavoussanakis, K., Lareau, L. F., Shah, P., & Wallace, E. W. J. (2022). Riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow. Bioinformatics, 38(8), 2358-2360. https://doi.org/10.1093/bioinformatics/btac093

@article{51d76a6a815a4636a48944a4d69e270f,

title = "Riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow",

abstract = "Motivation: Ribosome profiling, or Ribo-seq, is the state-of-the-art method for quantifying protein synthesis in living cells. Computational analysis of Ribo-seq data remains challenging due to the complexity of the procedure, as well as variations introduced for specific organisms or specialized analyses. Results: We present riboviz 2, an updated riboviz package, for the comprehensive transcript-centric analysis and visualization of Ribo-seq data. riboviz 2 includes an analysis workflow built on the Nextflow workflow management system for end-to-end processing of Ribo-seq data. riboviz 2 has been extensively tested on diverse species and library preparation strategies, including multiplexed samples. riboviz 2 is flexible and uses open, documented file formats, allowing users to integrate new analyses with the pipeline.",

author = "Cope, {Alexander L.} and Felicity Anderson and John Favate and Michael Jackson and Amanda Mok and Anna Kurowska and Junchen Liu and Emma Mackenzie and Vikram Shivakumar and Peter Tilton and Winterbourne, {Sophie M.} and Siyin Xue and Kostas Kavoussanakis and Lareau, {Liana F.} and Premal Shah and Wallace, {Edward W.J.}",

note = "Funding Information: This work was supported by the Biotechnology and Biological Sciences Research Council [BB/S018506/1 to E.W.J.W.] Publisher Copyright: {\textcopyright} 2022 The Author(s) 2022. Published by Oxford University Press.",

year = "2022",

month = apr,

day = "15",

doi = "10.1093/bioinformatics/btac093",

language = "English (US)",

volume = "38",

pages = "2358--2360",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "8",

}

Cope, AL, Anderson, F, Favate, J, Jackson, M, Mok, A, Kurowska, A, Liu, J, Mackenzie, E, Shivakumar, V, Tilton, P, Winterbourne, SM, Xue, S, Kavoussanakis, K, Lareau, LF, Shah, P & Wallace, EWJ 2022, 'Riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow', Bioinformatics, vol. 38, no. 8, pp. 2358-2360. https://doi.org/10.1093/bioinformatics/btac093

TY - JOUR

T1 - Riboviz 2

T2 - a flexible and robust ribosome profiling data analysis and visualization workflow

AU - Cope, Alexander L.

AU - Anderson, Felicity

AU - Favate, John

AU - Jackson, Michael

AU - Mok, Amanda

AU - Kurowska, Anna

AU - Liu, Junchen

AU - Mackenzie, Emma

AU - Shivakumar, Vikram

AU - Tilton, Peter

AU - Winterbourne, Sophie M.

AU - Xue, Siyin

AU - Kavoussanakis, Kostas

AU - Lareau, Liana F.

AU - Shah, Premal

AU - Wallace, Edward W.J.

N1 - Funding Information: This work was supported by the Biotechnology and Biological Sciences Research Council [BB/S018506/1 to E.W.J.W.] Publisher Copyright: © 2022 The Author(s) 2022. Published by Oxford University Press.

PY - 2022/4/15

Y1 - 2022/4/15

N2 - Motivation: Ribosome profiling, or Ribo-seq, is the state-of-the-art method for quantifying protein synthesis in living cells. Computational analysis of Ribo-seq data remains challenging due to the complexity of the procedure, as well as variations introduced for specific organisms or specialized analyses. Results: We present riboviz 2, an updated riboviz package, for the comprehensive transcript-centric analysis and visualization of Ribo-seq data. riboviz 2 includes an analysis workflow built on the Nextflow workflow management system for end-to-end processing of Ribo-seq data. riboviz 2 has been extensively tested on diverse species and library preparation strategies, including multiplexed samples. riboviz 2 is flexible and uses open, documented file formats, allowing users to integrate new analyses with the pipeline.

AB - Motivation: Ribosome profiling, or Ribo-seq, is the state-of-the-art method for quantifying protein synthesis in living cells. Computational analysis of Ribo-seq data remains challenging due to the complexity of the procedure, as well as variations introduced for specific organisms or specialized analyses. Results: We present riboviz 2, an updated riboviz package, for the comprehensive transcript-centric analysis and visualization of Ribo-seq data. riboviz 2 includes an analysis workflow built on the Nextflow workflow management system for end-to-end processing of Ribo-seq data. riboviz 2 has been extensively tested on diverse species and library preparation strategies, including multiplexed samples. riboviz 2 is flexible and uses open, documented file formats, allowing users to integrate new analyses with the pipeline.

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JO - Bioinformatics

JF - Bioinformatics

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ER -

Riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow

Abstract

All Science Journal Classification (ASJC) codes

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